Genome sequences of extant and extinct gibbons reveal their phylogeny, demographic history, and conservation status
Description
Genome annotation (GFF files) of four chromosome-level gibbon genomes and genome sequences of gibbon mitochondrial genomes.
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Genome Annotation: We identified repeat sequences using a combination of homology-based strategies and ab initio-based methods. We used LTR_Finder, GenomeTools (v1.6.1), LTR_retriever (v2.9.0) and RepeatModeler (v2.0.1) to build a de novo repeat library, and merged with RepBase dataset, then RepeatMasker was used to predict the repeats. For de novo gene structure prediction, AUGUSTUS (3.3.2) was used for de novo prediction. Protein-coding sequences of mouse (Mus musculus, GRCm38), human (Homo sapiens, GRCh38), chimpanzee (Pan troglodytes, GCF_002880755.1), gorilla (Gorilla gorilla, GCA_900006655.3) and orangutan (Pongo abelii, GCA_002880775.3) were used to homolog-based annotation using GeneWise (v2.4.1) , the final gene functional annotation were mapped to the following public databases: GO, KEGG, KOG, NR, PFAM, and TrEMBL. Mitochondrial genome assembly: The de novo genome assembly tool Novoplasty was used to construct the whole mitochondrial genomes from paired-end short reads. The complete mitochondrial sequence of the northern white-cheeked gibbon (N. leucogenys, GeneBank accession number: NC_021957) was used as a seed and reference input. Only complete circularized mitochondrial sequences were used for downstream analysis. For the mitogenome of Hainan gibbon, we performed the short-read mapping method to call the consensus sequence from BAM file using samtools. The whole mitogenome of an eastern black crested gibbon (Nomascus nasutus) was generated from DNA extracted from a fecal sample which has been collected in Trung Khanh Nature Reserve, Cao Bang Province, Vietnam in 2008. DNA was extracted with the Qiagen Stool Mini Kit. The whole mitogenome was generated via 20 overlapping PCR products with a length of 1.0-1.2 kb followed by Sanger sequencing.
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Funders
- Ministry of Science and Technology of the People's Republic of China (MOST)Grant ID: 2022YFF1301500
- Yunnan Revitalization Talent Support Program Young Talent Project